Project Summary/Abstract The characteristic findings in Alzheimer's disease (AD) post-mortem brain (PMB) are degeneration of neurons together with extensive amounts of amyloid deposits (A42) (a cleavage product of the amyloid precursor protein encoded by the APP gene) and tau (encoded by the MAPT gene). Cerebrospinal fluid (CSF) A42 and tau levels can predict AD but have a limited reliability in discriminating AD from other neurodegenerative diseases. The apolipoprotein (APOE) 4 allele and age are currently the only factors strongly associated with late onset AD. The large gaps in our understanding of the genetic aspects of AD may include additional genetic factors that impact age of onset and phenotypic expression of late onset AD. Individual genetic findings (non- synonomous SNPs) associated with complex diseases, such as AD, are unlikely to fully explain the substantial impact of genetic variation on disease pathogenesis. Multilevel etiologic factors are likely to underlie complex diseases and may include multiple loci within and surrounding a gene that influence regulation of transcription and post-transcription, emphasizing the need for integrative evaluation of large genetic regions and correlations with protein biomarker levels as a means for predicting disease risk. This proposal focuses on the overall hypothesis that multiple genetic loci surrounding and within large gene regions act to regulate gene expression in an AD specific manner. During the mentored phase (K99) of this investigation the first aim is to find multiple loci or combinations of SNPs (haplotypes) surrounding and within the APOE, APP and MAPT genes that correlate with expression levels in CSF and PMB. Candidate genetic and protein biomarkers will expand beyond APOE, APP and MAPT genes to include other genes likely to be biologically relevant to neurodegenerative disease. The second aim is to demonstrate that putative regulatory haplotypes functionally impact expression by utilizing genomic DNA, containing a particular putative regulatory haplotype, as the active site of gene regulation in reporter and minigene assays. During the independent phase (R00), the final aim is to test regulatory haplotypes for their reliability in discerning between different AD phenotypes and between AD and other neurodegenerative diseases. Collectively, these proposed experiments are unique because they go beyond the simple correlation between core promoter loci and biomarker expression levels by using a combination of genetic, statistical and functional techniques to evaluate the influence of multiple loci within putative distant regulatory elements on AD relevant gene expression to find haplotypes that predict AD. The research and career development components of this K99/R00 application will provide the necessary training for the applicant to become a successful independent investigator who can integrate these techniques to improve our understanding of neurodegenerative disease risk.